How Al-Qaeda Uses Encryption Post-Snowden

A question (disclaimer... I don't know much about encryption and assume types are recognizable to experts).

If Al-Quida has it's own type of encryption wouldn't that be a huge red flag as it went across the wires and the senders and recipients be fingered almost immediately?

It seems it would be safer to use something lots of other people are using as well.

I got this from Schneier's blog:

https://www.schneier.com/blog/archives/2014/05/new_al_qaeda_...